Summary

---
title: "COVID-19"
author: "Marcos Abreu"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    social: menu
    source_code: embed
    vertical_layout: fill
---

```{r setup, include=FALSE}
#---------------------- Update Data ------
library(flexdashboard)
devtools::install_github("RamiKrispin/coronavirus")
library(coronavirus)

data("coronavirus")

#------------------ Parameters ------------------
# Set colors
# https://www.w3.org/TR/css-color-3/#svg-color
confirmed_color <- "purple"
active_color <- "#1f77b4"
recovered_color <- "forestgreen"
death_color <- "red"
#countries <- c("Brazil", "Argentina", "Belgium", "Italy", "US")
countries <- c("Brazil")
```


```{r df_totals, include=FALSE}
#------------- Data - Total cases by country --------------
`%>%` <- magrittr::`%>%`
df_totals <- coronavirus %>% 
  dplyr::filter(Country.Region %in% countries) %>% 
  dplyr::group_by(Country.Region, type) %>% 
  dplyr::summarise(total = sum(cases)) %>% 
  tidyr::pivot_wider(names_from = type, 
                     values_from = total) %>% 
  dplyr::arrange(-confirmed) %>% 
  dplyr::ungroup() %>% 
  dplyr::mutate(country = Country.Region) %>% 
  dplyr::mutate(country = trimws(country)) %>% 
  dplyr::mutate(country = factor(country, levels = country))
```


```{r df_daily, include=FALSE}
#------------- Data - Total cases daily --------------
`%>%` <- magrittr::`%>%`
df_daily <- coronavirus %>% 
  dplyr::filter(Country.Region %in% c("Brazil")) %>% 
  dplyr::group_by(date, type) %>% 
  dplyr::summarise(total = sum(cases, na.rm = TRUE)) %>% 
  tidyr::pivot_wider(names_from = type, 
                     values_from = total) %>% 
  dplyr::arrange(date) %>% 
  dplyr::ungroup() %>% 
  dplyr::mutate(active = confirmed - death) %>% 
  dplyr::mutate(
    confirmed_cum = cumsum(confirmed),
    death_cum = cumsum(death),
    active_cum = cumsum(active)
  )


```


Summary
=======================================================================
Row
-----------------------------------------------------------------------
### confirmed {.value-box}

```{r}
valueBox(value = df_totals$confirmed, 
         caption = "Casos confirmados", 
         icon = "fas fa-user-md", 
         color = "purple")
```

### death {.value-box}
```{r}
valueBox(value = df_totals$death, 
         caption = "Casos confirmados", 
         icon = "fas fa-user-md", 
         color = "red")
```

Row
-----------------------------------------------------------------------

### **Daily cumulative cases by type** (Brazil)
```{r}
plotly::plot_ly(data = df_daily) %>%
  plotly::add_trace(
    x = ~date,
    y = ~confirmed_cum,
    type = "scatter",
    mode = "lines+markers",
    # name = "Active",
    name = "Confirmed",
    line = list(color = active_color),
    marker = list(color = active_color)
  ) %>%
  plotly::add_trace(
    x = ~date,
    y = ~death_cum,
    type = "scatter",
    mode = "lines+markers",
    name = "Death",
    line = list(color = death_color),
    marker = list(color = death_color)
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-02-04"),
    y = 1,
    text = paste("First case"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -10,
    ay = -90
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-11"),
    y = 3,
    text = paste("First death"),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -90,
    ay = -90
  ) %>%
  plotly::add_annotations(
    x = as.Date("2020-03-18"),
    y = 14,
    text = paste(
      "New containment",
      "",
      "measures"
    ),
    xref = "x",
    yref = "y",
    arrowhead = 5,
    arrowhead = 3,
    arrowsize = 1,
    showarrow = TRUE,
    ax = -10,
    ay = -90
  ) %>%
  plotly::layout(
    title = "",
    yaxis = list(title = "Cumulative number of cases"),
    xaxis = list(title = "Date"),
    legend = list(x = 0.1, y = 0.9),
    hovermode = "compare"
  )
```